Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting

Johannessen, Helen; Gill, Peter; Shantan, Gnanagowry; Fonneløp, Ane Elida

doi:10.1016/j.fsigen.2022.102750

Cited by 10 publications

(16 citation statements)

References 42 publications

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“…The first dataset (A) comprised 158 samples of low-level degraded DNA. This dataset was taken from a previous study described in detail by Johannessen et al[17]. It consists of samples taken in relation to simulated sexual assault: vaginal mucosa and epithelial cells were recovered from fin-gernail swabs, penile swabs and boxer-shorts.…”

Section: Relationship Between Dna Concentration Andmentioning

confidence: 99%

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

Gill

Bleka

Fonneløp

2022

Preprint

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The application of qPCR to estimate the quantity of DNA present is usually based upon a short amplicon (typically c.80bp) and a longer amplicon (typically c.200-300bp) where the latter is used to determine the amount of degradation present in a sample. The data are used to make decisions about a) whether there is sufficient template to amplify? b) how much of the elution volume to forward to PCR? A typical multiplex amplifies template in the region of 100-500bp. Consequently, the results from an 80bp amplicon will tend to overestimate the actual amplifiable quantity that is present in a degraded sample. To compensate, a method is presented that relates the quantity of amplifiable DNA to the average RFU of the amplified fragments. This provides greatly improved accuracy of the estimated quantity of DNA present, which may differ by more than an order of magnitude compared to qPCR. The relative DNA quantities can be apportioned per contributor once mixture proportions are ascertained with probabilistic genotyping software (EuroForMix). The motivation for this work was to provide an improved method to generate data to prepare distributions that are used to inform activity level propositions. However, other applications will benefit, particularly those where extraction and quantification are bypassed: For example direct PCR and Rapid DNA technology. The overall aim of this work was to provide a method of quantification that is standardised and can be used to compare results between different laboratories that use different multiplexes. A software solution "ShinyRFU" is provided to aid calculations.

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Section: Relationship Between Dna Concentration Andmentioning

confidence: 99%

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

Gill

Bleka

Fonneløp

2022

Preprint

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“…The types of cases were grouped in four categories; violent crime (21 cases), property crimes (21), sexual assault (17), and 'other' (6).…”

Section: What Types Of Cases Were Addressed?mentioning

confidence: 99%

“…• The interpretation of bodyfluid testing results. Particularly the; -prevalence of bodyfluids on bodyparts, including fingernails and genitalia, and underwear (note that a relevant study on this topic [17] was published after the report was issued), -probability of false positives of regularly used tests.…”

mentioning

confidence: 99%

Reporting on Forensic Biology Findings Given Activity Level Issues in the Netherlands

Kokshoorn

Luijsterburg

2022

SSRN Journal

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“…The first dataset (A) comprised 158 samples of low-level degraded DNA. This dataset was taken from a previous study described in detail by Johannessen et al[17]. It consists of samples taken in relation to simulated sexual assault: vaginal mucosa and epithelial cells were recovered from fingernail swabs, penile swabs and boxer-shorts.…”

Section: Relationship Between Dna Concentration Andmentioning

confidence: 99%

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

Gill

Bleka

Fonneløp

2021

Preprint

Self Cite

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A comparative study has been carried out, comparing two different methods to calculate activity level likelihood ratios (LRa) using Bayesian Networks. The first method uses the sub-source likelihood ratio (log10LRφ) as a 'quality indicator'. However, this has been criticised as introducing potential bias from population differences in allelic proportions. An alternative method has been introduced that is based upon the total RFU of a DNA profile that is adjusted, by multiplication, of the mixture proportion (Mx) which is calculated from quantitative probabilistic genotyping software (EuroForMix). Bayesian logistic regressions of direct transfer data showed that the two methods were comparable. Differences were attributed to sampling error, and small sample sizes of secondary transfer data. The Bayesian approach facilitates comparative studies by taking account of sampling error; it can easily be extended to compare different methods.

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Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting

Cited by 10 publications

References 42 publications

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

Reporting on Forensic Biology Findings Given Activity Level Issues in the Netherlands

Limitations of qPCR to estimate DNA quantity: An RFU method to facilitate inter-laboratory comparisons for activity level, and general applicability

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